The stewards judged that Hirvonen's Citroen DS3 was running with a non-homologated clutch and an oversized turbo component.
But the team's technical chief Xavier Mestelan-Pinon insisted that the parts offered no performance advantage.
"The scrutineers identified differences in between the homologation sheet and two components: the clutch and the turbocharger," he said.
"The Citroen DS3 WRC's clutch mechanisms are homologated with lightening holes. Our supplier recently provided us with a batch of parts that were not perforated and one of them was fitted to the #2 DS3 WRC.
"These parts don't provide any gain in terms of performance, as they are heavier than those which are homologated.
"Regarding the turbocharger, which is a standard part on all World Rally Cars, the wheel turbine dimension exceed the maximum authorised. This difference comes from dilatation, as the wheel is subject to extreme temperature and rpm factors."
Team boss Yves Matton felt the ruling was unfair.
"We had no intention whatsoever to cheat and the decision appears out of proportion," he said.
"Given the fact that the reported differences didn't bring us any advantage, we've decided to appeal."
Matton also apologised to Hirvonen and co-driver Jarmo Lehtinen for the situation.
"At the moment, most of all I feel sorry for Mikko Hirvonen and Jarmo Lehtinen, who produced a superb performance on a particularly difficult rally," said Matton.
"They really deserved their first win with us. All I can do, on behalf of the entire team, is offer my sincere apologies for this situation. I hope that Mikko and Jarmo will have the chance to top the podium again very soon."
Hirvonen's exclusion made Mads Ostberg the rally winner for Adapta Ford.